Highly sensitive extraction-free saliva-based molecular assay for rapid diagnosis of SARS-CoV-2

• Published in: Journal of clinical microbiology 2024-06, Vol.62 (6), p.e0060024
• Main Authors: Margulis, Michael, Rohana, Hanan, Erster, Oran, Mandelboim, Michal, Biber, Asaf, Schwartz, Eli, Peretz, Avi, Danielli, Amos
• Format: Article
• Language: English
• Subjects: Adult; Aged; Clinical Microbiology; COVID-19 - diagnosis; COVID-19 Nucleic Acid Testing - methods; Female; Humans; Innovative Diagnostic Methods; Israel; Male; Middle Aged; Molecular Diagnostic Techniques - methods; Molecular Diagnostic Techniques - standards; Nasopharynx - virology; Saliva - virology; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Sensitivity and Specificity; Specimen Handling - methods
• ISSN: 0095-1137; 1098-660X; 1098-660X
• DOI: 10.1128/jcm.00600-24

The COVID-19 pandemic highlighted the necessity of fast, sensitive, and efficient methods to test large populations for respiratory viruses. The "gold standard" molecular assays for detecting respiratory viruses, such as quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR), rely on invasive swab samples and require time-consuming and labor-intensive extraction processes. Moreover, the turnaround time for RT-qPCR-based assays is too lengthy for rapid screening. Extraction-free saliva-based methods provide a non-invasive sampling process with a fast turnaround time and are suitable for high-throughput applications. However, when used with a standard RT-qPCR system, the absence of extraction significantly reduces the assays' sensitivity. Here, using a novel optical modulation biosensing (OMB) platform, we developed a rapid and highly sensitive extraction-free saliva-based molecular assay. We blindly tested 364 paired nasopharyngeal swabs and saliva samples from suspected SARS-CoV-2 cases in Israel. Compared with the gold standard swab-based RT-qPCR assay, the sensitivity of the extraction-free saliva-based OMB assay is 90.7%, much higher than the sensitivity of extraction-free saliva-based RT-qPCR assay (77.8%) with similar specificity (95.3% and 97.6%, respectively). Moreover, out of 12 samples identified by the OMB-based assay as positive, 8 samples were collected from hospitalized patients in a COVID-19 ward and were verified to be SARS-CoV-2-positive upon admission, indicating that the actual clinical sensitivity and specificity of the OMB assay are higher. Considering its user-friendly saliva-based protocol, short and cost-effective extraction-free process, and high clinical accuracy, the OMB-based molecular assay is very suitable for high-throughput testing of large populations for respiratory viruses. Three years after the SARS-CoV-2 outbreak, there are no molecular tests that combine low-cost and straightforward sample preparation, effective sample handling, minimal reagent and disposable requirements, high sensitivity, and high throughput required for mass screening. Existing rapid molecular techniques typically sacrifice certain requirements to meet others. Yet, localized outbreaks of novel viral diseases happen daily in different parts of the world. In this context, respiratory diseases are of specific importance, as they are frequently airborne and highly contagious, with the potential for a rapid global spread. T